chr12-85656406-T-C

Variant names:

• chr12-85656406-T-C
• rs7304475

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.44 in 152,058 control chromosomes in the GnomAD database, including 15,189 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.44 (15189 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66786 AN: 151940 Hom.: 15175 Cov.: 33

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.421

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.440 AC: 66836 AN: 152058 Hom.: 15189 Cov.: 33 AF XY: 0.438 AC XY: 32588 AN XY: 74318

African (AFR) AF: 0.556 AC: 23076 AN: 41478

American (AMR) AF: 0.386 AC: 5893 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1522 AN: 3466

East Asian (EAS) AF: 0.525 AC: 2710 AN: 5158

South Asian (SAS) AF: 0.432 AC: 2088 AN: 4830

European-Finnish (FIN) AF: 0.374 AC: 3945 AN: 10552

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26316 AN: 67978

Other (OTH) AF: 0.420 AC: 886 AN: 2110

Alfa AF: 0.416 Hom.: 1679

Bravo AF: 0.448

Asia WGS AF: 0.457 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.51
PhyloP100		0.093

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7304475; hg19: chr12-86050184;